The Latin names commonly used for most of these nuclei are grammatically and orthographically incorrect. Latin grammar would require to use the genitive caseraphes ('of the seam') instead of the nominative caseraphe ('seam') in these Latin expressions. The main authority in anatomical names, Terminologia Anatomica uses for example nucleus raphes magnus[6] instead of the grammatically incorrect nucleus raphe magnus. The spelling raphe/raphes however can also be contested as numerous sources[7][8][9] indicate that raphe is an incorrect Latin rendering of the Ancient Greek word ῥαφή as the initial letter rho with rough breathing (spiritus asper) is normally rendered as rh in Latin.[7] The edition of the Nomina Anatomica that was ratified in Jena in 1935 used rhaphe instead of raphe.[10][11]

The raphe nuclei have a vast impact upon the central nervous system. Many of the neurons in the nuclei (but not the majority) are serotonergic; i.e., contain serotonin, a type of monoamine neurotransmitter and are modulated through fibrous pathways in the midbrain.[14]

Projections from the raphe nuclei also terminate in the dorsal horn of spinal gray matter where they regulate the release of enkephalins, which inhibit pain sensation.

The raphe nuclei provide feedback to the suprachiasmatic nuclei (SCN), thus contributing in circadian rhythms in animals. The SCN transmits to the raphe nuclei via the dorsomedial hypothalamus nucleus altering serotonin levels for sleep/wake states. The raphe nuclei will then transmit feedback to the SCN about the animal's vigilance and levels of alertness. This reciprocal feedback between the two structures provides an adaptable yet stable basis of circadian rhythms.[15]

More recent studies of the Raphe Nuclei done with rats involve the effects of Ghrelin on the Dorsal Raphe Nucleus. When administered, larger doses of Ghrelin act centrally on the raphe nucleus, hippocampus, and amygdala which causes dramatic increases in food intake, memory retention, and increases in anxiety. The effects of ghrelin on the raphe nucleus as soon as an hour after injection, suggesting rapid changes in the nucleus' structure. Changes also occur after 24 hours suggesting delayed modifications as well.[16]

^Foster, F.D. (1891-1893). An illustrated medical dictionary. Being a dictionary of the technical terms used by writers on medicine and the collateral sciences, in the Latin, English, French, and German languages. New York: D. Appleton and Company.